Inferring human phenotype networks from genome-wide genetic associations

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7833 LNCS, Issue , 2013, Pages 23-34

  Darabos, Christian ^a   Desai, Kinjal ^a   Cowper Sallari, Richard ^a   Giacobini, Mario ^b   Graham, Britney E ^a   Lupien, Mathieu ^c,d   Moore, Jason H ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF TURIN   (Italy)

^c PRINCESS MARGARET HOSPITAL   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BEHAVIORAL TRAITS; CURRENT LIMITATION; DEGREE DISTRIBUTIONS; GENETIC INTERACTION; GENOME-WIDE ASSOCIATION STUDIES; INTERACTING ELEMENTS; SCALE-FREE REGIONS; STANDARD COMMUNITIES;

BIOINFORMATICS; DATA MINING; ELECTRIC NETWORK TOPOLOGY; GENES; LEARNING SYSTEMS;

DIAGNOSIS;

EID: 84875085111     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-37189-9_3     Document Type: Conference Paper

References (25)

1. Akiyama, H., Barger, S., Barnum, S., Bradt, B., Bauer, J., Cole, G.M., Cooper, N.R., Eikelenboom, P., Emmerling, M., Fiebich, B.L., Finch, C.E., Frautschy, S., Griffin, W., Hampel, H., Hull, M., Landreth, G., Lue, L.-F., Mrak, R., Mackenzie, I.R., McGeer, P.L., O'Banion, M., Pachter, J., Pasinetti, G., Plata-Salaman, C., Rogers, J., Rydel, R., Shen, Y., Streit, W., Strohmeyer, R., Tooyoma, I., Muiswinkel, F.L.V., Veerhuis, R., Walker, D., Webster, S., Wegrzyniak, B., Wenk, G., Wyss-Coray, T.: Inflammation and alzheimer's disease. Neurobiology of Aging 21(3), 383-421 (2000)
2. Albert, R.: Scale-free networks in cell biology. J. of Cell Science 118, 4947-4957 (2005)
3. Barrenas, F., Chavali, S., Holme, P., Mobini, R., Benson, M.: Network properties of complex human disease genes identified through genome-wide association studies. PLoS ONE 4(11), e8090 (2009)
4. Bin, J., Bernatsky, S., Gordon, C., Boivin, J.-F., Ginzler, E., Gladman, D., Fortin, P.R., Urowitz, M., Manzi, S., Isenberg, D., Rahman, A., Petri, M., Nived, O., Sturfeldt, G., Ramsey-Goldman, R., Clarke, A.E.: Lung cancer in systemic lupus erythematosus. LungCancer 56(3), 303-306 (2007)
5. Blondel, V.D., Guillaume, J.-L., Lambiotte, R., Lefebvre, E.: Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment 2008(10), P10008+ (2008)
6. Falconer, D.S., Mackay, T.F.C.: Introduction to Quantitative Genetics, 4th edn. Prentice Hall (February 1996)
7. Goh, K.-I., Cusick, M.E., Valle, D., Childs, B., Vidal, M., Barabasi, A.-L.: The human disease network. Proceedings of the National Academy of Sciences 104(21), 8685-8690 (2007)
8. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S., Manolio, T.A.: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U S A 106(23), 9362-9367 (2009)
9. The International HapMap Consortium: A haplotype map of the human genome. Nature 437(7063), 1299-1320 (2005)
10. Jobin, C., Sartor, R.B.: Nf-kappab signaling proteins as therapeutic targets for inflammatory bowel diseases. Inflamm. Bowel Dis. 6(3), 206-213 (2000)
11. Kok, E.H., Alanne-Kinnunen, M., Isotalo, K., Luoto, T., Haikonen, S., Goebeler, S., Perola, M., Hurme, M.A., Haapasalo, H., Karhunen, P.J.: Crp gene variation affects early development of alzheimer's disease-related plaques. J. Neuroinflammation 8, 96 (2011)
12. Krum, S.A., Chang, J., Miranda-Carboni, G., Wang, C.-Y.: Novel functions for nfkappab: inhibition of bone formation. Nat. Rev. Rheumatol. 6(10), 607-611 (2010)
13. Li, H., Lee, Y., Chen, J.L., Rebman, E., Li, J., Lussier, Y.A.: Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. Journal of the American Medical Informatics Association: JAMIA 19(2), 295-305 (2012)
14. Loscalzo, J., Barabasi, A.-L.: Systems biology and the future of medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 3(6), 619-627 (2011)
15. McCarthy, M.I., Abecasis, G.R., Cardon, L.R., Goldstein, D.B., Little, J., Ioannidis, J.P.A., Hirschhorn, J.N.: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9(5), 356-369 (2008)
16. Newman, M.: Networks: An Introduction. Oxford University Press, Inc., New York (2010)
17. Osborne, C.K.: Steroid hormone receptors in breast cancer management. Breast Cancer Res. Treat. 51(3), 227-238 (1998)
18. Roubenoff, R., Drew, H., Moyer, M., Petri, M., Whiting-O'Keefe, Q., Hellmann, D.B.: Oral cimetidine improves the accuracy and precision of creatinine clearance in lupus nephritis. Ann. Intern. Med. 113(7), 501-506 (1990)
19. Sirota, M., Dudley, J.T., Kim, J., Chiang, A.P., Morgan, A.A., Sweet-Cordero, A., Sage, J., Butte, A.J.: Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci. Transl. Med. 3(96), 96-477 (2011)
20. Smith, E.P., Boyd, J., Frank, G.R., Takahashi, H., Cohen, R.M., Specker, B., Williams, T.C., Lubahn, D.B., Korach, K.S.: Estrogen resistance caused by a mutation in the estrogen-receptor gene in a man. N. Engl. J. Med. 331(16), 1056-1061 (1994)
21. Suthram, S., Dudley, J.T., Chiang, A.P., Chen, R., Hastie, T.J., Butte, A.J.: Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput. Biol. 6(2), e1000662 (2010)
22. Watts, D.J.: Small Worlds: The Dynamics of Networks Between Order and Randomness. Princeton University Press, Princeton (1999)
23. Watts, D.J., Strogatz, S.H.: Collective dynamics of "small- world" networks. Nature 393, 440-442 (1998)
24. Wu, X., Jiang, R., Zhang, M.Q., Li, S.: Network-based global inference of human disease genes. Mol. Syst. Biol. 4, 189 (2008)
25. Zhang, X., Cowper-Sal lari, R., Bailey, S.D., Moore, J.H., Lupien, M.: Integrative functional genomics identifies an enhancer looping to the sox9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 22(8), 1437-1446 (2012)